The Real Madrid star scored his fourth goal of the tournament as Fernando Santos' side picked up their first win from two outings and position themselves as the favourites to top their group.
It would be referee Geiger who stole the headlines, however, as he allegedly requested to keep the shirt of Ronaldo's Portugal team-mate Pepe.
The defender has spent his career in trouble with officials and was once again in the spotlight during Wednesday tie.
After a coming together with Diego Costa in Portugal's opener with Spain, the former Real Madrid centre-back was accused of diving following a pat on the back from Medhi Benatia in Moscow.
And, despite the play-acting, Geiger was all too happy to request his jersey following the full-time whistle.
"It's incredible, I do not know what this American referee is used to," Morocco winger Amrabat told the NOS. "He was very impressed by Cristiano Ronaldo, and I heard from Pepe that he asked for Pepe's shirt in the first half.
"Come on, man, we're here at a World Cup, it's not a circus!"
Amrabat and his Morocco team-mates were beaten for a second time in Russia, having lost their World Cup opener against Iran to an injury-time own-goal.
The 31-year-old was a doubt to feature in the meeting with Portugal on Wednesday as a result of a head injury picked up in the game prior but played the full 90 minutes wearing a scrum cap as protection.
"It was so hot, the sweat came down and the helmet was also tight," Amrabat said, while explaining that he could not remember anything about the opening game against Iran.
"From the first minute to the moment I woke up in the hospital, I wanted to play today, I felt good, even though I feel more tired than normal.
"It's now time to rest, recover and close the World Cup in a good way."
Morocco end their World Cup campaign against Spain on June 25, looking to sign out of Russia with at least a goal to their name.